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Article

Effects of Tropical Typical Organic Materials on Soil Physicochemical Properties and Microbial Community Structure

by
Shuhui Song
,
Siru Liu
,
Yanan Liu
,
Weiqi Shi
* and
Haiyang Ma
*
Key Laboratory of Tropical Crops Nutrition of Hainan Province, South Subtropical Crops Research Institute of Chinese Academy of Tropical Agricultural Sciences, Shetan Road 5, Xiashan District, Zhanjiang 524091, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(5), 1073; https://doi.org/10.3390/agronomy15051073
Submission received: 28 March 2025 / Revised: 26 April 2025 / Accepted: 26 April 2025 / Published: 28 April 2025
(This article belongs to the Section Agroecology Innovation: Achieving System Resilience)
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Abstract

:
Background: Returning pineapple leaves (PAL), banana stems (BAS), coconut husks (CCH), and organic fertilizer (OF) to the field is an important method for soil improvement. However, the effects of these materials on the soil remain unclear. Methods: This study employed a nylon-bag experiment filled with the above-mentioned materials to investigate the impacts on soil physicochemical properties and microbial community structure. Results: The short term acidification caused by PAL was due to the significant increase in isobutyric, isovaleric, and hexanoic acids. PAL and BAS promoted the formation of >0.25 mm aggregates in the short term (90 days). C and N were most abundant in <0.053 mm and 0.053–0.25 mm soil aggregates, while 13C and 15N were mainly enriched in 0.25–2 mm and >2 mm soil aggregates. The dominant biomarkers in the soil treated with PAL were Koribacteraceae, Chrysozymaceae, Trimorphomycetaceae, and Tremellales. The main biomarkers of soil treated with BAS were Caulobacteraceae, Aspergillaceae, Onygenales, and Ceratostomataceae. The dominant biomakers in the soil treated with CCH and OF were richer than those in soil treated with PAL and BAS. Conclusions: The long term return effects of CCH and OF are better than those of PAL and BAS.

1. Introduction

Latosols, which are widely distributed in tropical and subtropical regions, play a crucial role in the global carbon (C) and nitrogen (N) cycling. These soils are sensitive to external material inputs, characterized by high weathering degrees, low nutrient holding capacities, and distinct physical and chemical properties [1]. Organic matter plays a crucial role in soil, exerting a profound influence on its physical, chemical, and biological properties, thus determining soil fertility and health. Multiple studies highlighted how organic matter affects soil structure through aggregation mechanisms, impacts chemical reactions such as cation exchange, and stimulates biological activities in the soil ecosystem [2,3].
Soil pH is a crucial factor influencing soil fertility, nutrient availability, and microbial activity. The addition of organic materials to the soil, such as crop residues, manures, and compost, can significantly impact soil pH, often leading to notable shifts in the soil’s chemical environment [4,5,6]. The impact of organic matter on soil pH can vary depending on the nature of the organic materials. For instance, fresh crop residues typically undergo decomposition by soil microorganisms. During this process, organic acids may be produced as intermediate byproducts [7]. In some cases, the decomposition of nitrogen-rich crop residues can lead to the release of ammonium ions (NH4+). These NH4+ are further oxidized by nitrifying bacteria in the soil, a process that generates hydrogen ions (H+). The increased concentration of H+ can lower the soil pH, resulting in soil acidification [8,9,10]. In acid soils, organic matter can increase the soil pH by providing exchangeable cations such as calcium (Ca2+), magnesium (Mg2+), and potassium (K+). These cations can displace hydrogen ions from the soil exchange complex, thereby raising the soil pH [11,12,13].
Studies have also demonstrated that organic materials with different carbon-to-nitrogen (C:N) ratios lead to varied patterns of carbon and nitrogen allocation in the soil. Organic pig manure had the most significant impact on the soil microbial biomass nitrogen and dissolved total nitrogen, with increases of 49.3% and 50.7%, respectively [14,15]. Organic materials with a high C:N ratio, such as woody plant residues, tend to cause a temporary immobilization of N in the soil during decomposition. Microorganisms utilize the available N to break down the high-carbon-content materials, resulting in a decrease in the amount of available N for plants in the short term [15]. In contrast, organic materials with a low C:N ratio, such as fresh legume residues, can enhance N mineralization, releasing more N into the soil solution, which is beneficial for plant growth and can also affect the long term carbon sequestration potential in the soil [16]. Organic materials and chemical fertilization can lead to shifts in the composition of bacterial functional groups and have a notable influence on soil fungal community structure [17,18]; for example, organic matter addition significantly increases soil fungal richness [19].
The application of organic materials can also affect the abundance of plant-pathogenic fungi, and the use of organic amendments reduced the relative abundance of certain pathogenic fungi [20]. Organic materials can stimulate the growth of beneficial microorganisms, which may compete with pathogenic fungi for resources or produce antimicrobial substances, thereby suppressing the growth of pathogens. This reduction in pathogenic fungi can contribute to improved plant health and reduced disease incidence in orchards. Although less studied compared to bacteria and fungi, actinomycetes are also affected by organic materials. Some research has shown that the addition of organic materials rich in lignocellulose, such as wood chips or straw, can increase the abundance of actinomycetes in the soil. Actinomycetes are important for the decomposition of complex organic compounds, and the high-cellulose-containing organic materials provide a suitable substrate for their growth and activity [21]. The microbial community in lateritic soil is a crucial component of soil ecosystems, being responsible for key biochemical processes including, organic matter decomposition, nutrient cycling, and soil structure formation. The addition of typical tropical organic materials can substantially alter the microbial community structure by providing diverse carbon and energy sources. Some organic materials may preferentially support the growth of specific microbial groups, such as bacteria or fungi, thus changing the relative abundance and composition of the microbial community [22].
Despite the growing body of knowledge on the impacts of organic materials on soil carbon and nitrogen allocation and microbial communities in general soil types, there is still a lack of comprehensive studies specifically focusing on lateritic soils in tropical regions. Pineapple leaves (PAL), banana stems (BAS), and coconut husks (CCH) are typical organic materials in the tropics, and the application of organic materials, including organic fertilizer (OF), is the key measure to improve the physical and chemical properties of soil. However, the effects of the above-mentioned organic materials on the physical and chemical properties of the soil and the microbial community remain unclear. Therefore, this study aims to (1) evaluate the improvement effect of typical tropical organic materials on acidified soil, (2) clarify the effects of returning typical tropical organic materials to the field on the microbial community in latosol, and (3) screen for excellent types of organic materials for soil improvement. Understanding the effects of typical tropical organic materials on carbon and nitrogen allocation and microbial community structure in lateritic soil is essential for effective soil fertility management, enhancing soil carbon sequestration, and maintaining the stability and functionality of soil ecosystems in these regions.

2. Materials and Methods

2.1. Site Description

The field experimental sites were located at the National Agricultural Experimental Station for Soil Quality in Zhanjiang (47°26′ N, 126°38′ E) of Guangdong province in South China, where the temperature oscillates between 22.7 °C and 23.5 °C. The average annual rainfall is 1395.5 to 1723.1 mm, and the average annual sunshine duration is 1714.8 to 2038.2 h. During the test period, the soil temperature in the test field ranged from a low of 17.6 °C to a high of 25.7 °C, with an average of 20.7 °C. The previous crop was sweet maize, and in the test year, corn was planted in the surrounding areas except for the experimental area. At the site, soil samples of 0–20 cm deep were taken randomly from arable land with sweet maize cropping. The soil samples were air-dried and ground to pass a 2-mm sieve for chemical and physical analysis. The <2 mm soil samples were further ground to pass through a 0.15-mm sieve to measure soil total C and total N contents by an element analyzer. Basic physical and chemical soil properties before the experiment were as follows. pH: 5.74, EC: 40.30 μs/cm, available P: 14.32 mg/kg, available K: 73.63 mg/kg, soil alkaline N: 88.54 mg/kg, exchangeable Ca: 443.08 mg/kg, exchangeable Mg: 75.09 mg/kg, available Mn: 33.92 mg/kg, available Fe: 15.00 mg/kg, available Cu: 1.50 mg/kg, available Zn: 0.87 mg/kg, C: 1.21%, N: 0.09%, δ13C: −20.79, δ15N: 6.98.

2.2. Pot Experiment in the Field

Organic materials were pineapple leaf (PAL), banana stems (BAS), coconut husk (CCH), and organic fertilizer (OF). Soil without organic materials was used as CK. Pineapple leaf (PAL) and banana stems (BAS) were collected from the experimental field of the South Subtropical Crops Research Institute of the Chinese Academy of Tropical Agricultural Sciences. Coconut husk (CCH) and organic fertilizer (OF) were commodity materials. The materials were air-dried and chopped by a crop cutter into 1–2 cm pieces. The original materials were ground with a ball mill to measure total C and N contents by an element analyzer (Elementar Vario UNICUBE, Elementar, Shanghai, China). (NH4)2SO4 was used to adjust the origin C/N ratio with 23. The properties, dosage of organic materials, and ammonium sulfate dosage are shown in Table 1.
Nylon litterbags in the size of 10 cm long × 10 cm wide and having apertures of 200 mesh were used in this study. Such a mesh size was considered to prevent soil particle exchanges but allow water and microbial exchanges between inside and outside the nets. The soil bulk density was as high as 1.0–1.1 g cm−3, similar to that of the surrounding soil. 250.0 g (dry basis) of soil and organic materials were filled into each nylon litterbag, and the amounts of organic materials were shown in Table 1. The litterbags were placed at 20 cm depth and covered with soil. No crops were grown to avoid root disturbance in the plot (80 m2) where the litterbags were placed. 16 nylon litterbags per treatment were prepared.
For each treatment, 4 bags of samples were taken out each time, and the sampling was carried out 4 times (90 days, 180 days, 270 days, and 1080 days) during the observation period until the experiment ended in November 2023. During sampling, carefully take out the nylon mesh bags of each treatment and use a brush to remove the soil adhering to the surface of the nylon mesh bags. Take 150 g of the air-dried soil, grind it, and sieve it through 2 mm and 100-mesh sieves, respectively, for the physical and chemical analysis. Additionally, take 100 g of the soil and place it in a refrigerator at −20 °C for storage, which will be used for analyzing the soil microbial community and enzyme activity.

2.3. Analysis of Soil pH/EC, Ca/Mg, Total C, and N

Soil pH/EC in water (1:2.5) was measured by a pH meter. Exchangeable Ca and Mg in soil were determined by the titration method [23]. The <2 mm soil samples were further ground to pass through a 0.15-mm sieve to measure soil total C and total N contents by an element analyzer (Elementar Vario UNICUBE, Elementar, Shanghai, China).

2.4. Soil Organic Acids Analysis

Soil organic acids analysis refers to the literature by Han et al. (2013) [24] and Khan et al. (2020) [25].

2.5. Soil Aggregate Structure

Assemble a set of sieves with mesh sizes of 2 mm, 0.25 mm, and 0.053 mm and place them in a sieve shaker. Take 50 g of the prepared soil sample and place on the top sieve. Wet the sample thoroughly with distilled or deionized water, then let it stand for a few minutes for water penetration. Immerse the sieves in water, ensuring complete submersion. Operate the sieve shaker at 45 oscillations per minute for 5 min. After sieving, remove the sieves, gently wash the aggregates on each sieve to remove adhered fine particles, transfer them to pre-weighed containers, and dry in an oven at 105 °C until constant weight. Weigh the containers with dried aggregates to determine the weight of each size fraction. Calculate the percentage of aggregates in each fraction based on the original sample weight and analyze the distribution to evaluate soil structure and stability.

2.6. FTIR Analysis

1 mg of the sieved soil was mixed thoroughly with potassium bromide (KBr) with a ratio of about 1:100. The mixed sample of soil and KBr is pressed into a thin pellet using a pellet press. The infrared spectrometer emits infrared light and scans the sample within a certain wavelength range from 4000 cm−1 to 400 cm−1. Analyze the obtained infrared spectrum and identify the characteristic absorption peaks of different functional groups and minerals in the soil.

2.7. Methods of Microbial Amplicon Sequencing Experiment

Soil genomic DNA was extracted using the E.Z.N.A. Soil DNA Kit (Omega Bio-tek, Inc., Norcross, GA, USA) following the manual. Concentration and quality of the genomic DNA were checked by NanoDrop 2000 spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA). DNA samples were stored at −20 °C for subsequent experiments. The V3-V4 hypervariable region of the bacterial 16S rRNA gene and the ITS region were amplified with the universal primers 338F (5′-ACTCCTACGGGAGGCAGCAG-3′), 806R (5′-GGACTACNNGGGTATCTAAT-3′), and ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′). For each sample, an 8-digit barcode sequence was added to the 5′ end of the forward and reverse primers (provided by Allwegene Company, Beijing, China). The PCR was carried out on an ABI 9700 PCR instrument (Applied Biosystems, Foster City, CA, USA) using 25 μL reaction volumes, containing 12.5 μL 2× Taq PCR MasterMix (Vazyme Biotech Co., Ltd., Nanjing, China), 3 μL BSA(2 ng/μL), 1 μL Forward Primer(5 μM), 1 μL Reverse Primer(5 μM), 2 μL template DNA, and 5.5 μL ddH2O. Cycling parameters were 95 °C for 5 min, followed by 28 cycles of 95 °C for 45 s, 55 °C for 50 s, and 72 °C for 45 s, with a final extension at 72 °C for 10 min. The PCR products were purified using an Agencourt AMPure XP Kit (Beckman Coulter, Inc., Brea, CA, USA). Sequencing libraries were generated using the NEB Next Ultra II DNA Library Prep Kit (New England Biolabs, Inc., Ipswich, MA, USA) following the manufacturer’s recommendations. The library quality was assessed by Nanodrop 2000 (ThermoFisher Scientific, Inc., USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA), and ABI StepOnePlus Real Time PCR System (Applied Biosystems, Inc., USA), successively. Deep sequencing was performed on the Illumina Miseq/Nextseq 2000/Novaseq 6000 (Illumina, Inc., San Diego, CA, USA) platform at Beijing Allwegene Technology Co., Ltd. (Beijing, China). After the run, image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline Version 2.6 (Illumina, Inc., USA). Databases of bacteria 16s and fungus ITS were Silva 138 and Unite v8.2, respectively.

2.8. Statistics

Microsoft Excel 2021 was used for data analysis and processing. All the plots were drawn using Origin 2021. A one-way analysis of variance (ANOVA) and a least significant difference (LSD) were used to test the differences among treatments at a 5% significance level (p < 0.05) using SPSS 23.0.

3. Results

3.1. Soil pH/EC and Organic Acid Content Changes

It can be seen from Table 2 that without organic material input, there is no significant change in the soil pH value. For 90 days, the pH values of the soils treated with PAL and CCH were significantly lower than that of CK-treated soil. However, after 1080 days, the pH values of the soils treated with PAL and CCH were higher than that of CK-treated soil. The pH value of the soil with the mixture of BAS and OF cultured for 90 days was significantly higher than that of CK. However, as the culture time extended to 1080 days, the pH value of the soil treated with BAS decreased and was significantly lower than that of the CK treatment. The pH value of the soil with OF treatment also decreased gradually with the cultivation time, yet it was still significantly higher than that of the CK treatment.
The electrical conductivity of the soils treated with PAL, BAS, and CCH for 90 d was the highest and significantly higher than that of the OF treatment and the CK treatment, while the electrical conductivity of the CK treatment was the lowest. Compared with the 90 d culture, the conductivity of the soil in the 1080 d slightly decreased, and the conductivity of the soils cultured with organic materials decreased significantly. At 1080 d, the conductivity of the soil cultured with BAS was significantly higher than that of the soil treated with PAL and CCH, but there was no significant difference between its conductivity and that of the soil treated with OF. The exchangeable Ca content was higher in the soil cultured with PAL and BAS, and the exchangeable Mg content was higher in the soil cultured with CCH and BAS.
Further analysis showed that there were 11 kinds of organic acids (shikimic acid, lactic acid, propionic acid, isobutyric acid, succinic acid, isovaleric acid, adipic acid, fumaric acid, benzoic acid, oxalic acid, and hexanoic acid) in the soil (Figure 1). The contents of isovaleric acid, lactic acid, and isobutyric acid in the soil after 90-day incubation were significantly higher than those of other organic acids. The main types of organic acids in the soil after 1080 days of incubation were lactic acid, isovaleric acid, and oxalic acid.

3.2. Changes of Aggregate Structure

After 90 days of cultivation, the proportion of aggregates larger than 0.25 mm increased significantly in the soils treated with PAL and BAS. The proportion of 0.25–0.053 mm aggregates was significantly lower compared to that in the soils treated with CCH, OF, and CK. Moreover, the proportion of aggregates smaller than 0.053 mm decreased significantly in the soils treated with organic materials (Figure 2). These results indicated that organic materials promoted the transformation of micro-aggregates into macro-aggregates.
Until 270 days of cultivation, PAL still had a relatively significant impact on the formation of soil aggregates, and the effect of organic fertilizer on soil aggregate formation gradually became apparent. There was no significant difference in the proportion of aggregates >0.25 mm between the soils treated with PAL and OF, but both were significantly higher than those in other treatments. As the cultivation time extended to 540 days and 1080 days, PAL no longer had an obvious advantage in the formation of >0.25 mm soil aggregates. In contrast, the effect of OF continued to persist and was significantly higher than that of other treatments. Additionally, the proportion of >0.25 mm soil aggregates treated with organic materials was still significantly higher than that of CK.

3.3. Distribution of C and N in Soil Aggregates

The C and N contents in aggregates smaller than 0.053 mm and in the 0.053–0.25 mm size range were higher (Figure 3), and the C and N contents in aggregates smaller than 0.053 mm were the highest. The application of organic materials significantly increased the C and N contents in soil aggregates. Organic materials made significant contributions to the C content in aggregates smaller than 0.053 mm and those in the 0.053–0.25 mm range. The C content in all aggregates gradually decreased with the extension of cultivation time. At 1080 days, the N content in the soil aggregates <0.053 mm treated with CCH increased significantly, while the N contents in aggregates of other particle sizes gradually decreased with the cultivation time.
A further analysis of the changes in 13C and 15N in aggregates of different particle sizes (Figure 4) revealed that, after 90 days of soil-mixing cultivation, the 13C and 15N values in soil aggregates <0.053 mm and in the 0.053–0.25 mm range were significantly higher than those in soil aggregates <0.053 mm and >2 mm. As the cultivation time progressed, 13C and 15N tended to become enriched in aggregates, and this enrichment was more pronounced in soil aggregates >2 mm.

3.4. Infrared Structure of Aggregates

The chemical structure of organic carbon in soil aggregates was altered by the addition of organic material (Figure 5 and Figure 6). After 90 days, there was a significant impact on the functional groups of organic carbon in 0.25–2 mm and >2 mm soil aggregates. The organic-carbon functional groups in <0.053 mm and 0.053–0.25 mm aggregates were significantly affected at 1080 days. Under the CCH treatment, the peak intensity of the functional groups C=O/C–C, C–N/C–O/C–F/C–C, C=C/N–H, and OH/C–H in <0.053 mm soil aggregates decreased (Figure 5a). As the cultivation time progressed, the peak intensity of these functional groups, namely C=O/C–C, C–N/C–F/C–C, C=C/N–H, and OH/C–H, decreased until 1080 days (Figure 6a). There was no significant difference in the effects of different organic materials on the functional groups in <0.053 mm aggregates. The vibration of the functional groups in the <0.053 mm aggregates was significantly weakened under the treatment of other organic materials, except that of OF and CK. After 90 days, the vibration of the functional groups C=C/N=H and –OH/C–H in 0.053–0.25 mm soil aggregates were enhanced. After 1080 days, the vibration strength of the functional groups C=C/N=H and –OH/C–H in 0.053–0.25 mm soil aggregates were significantly stronger than that of other treatments. The vibration intensity of C=C/N=H in 0.25–2 mm aggregates and >2 mm treated with PAL, BAS, and CCH was significantly enhanced after 90 days. After 1080 days of cultivation, the vibration intensity of C=C/N=H in 0.25–2 mm and >2 mm aggregates treated with PAL, BAS, and CCH decreased compared with CK.

3.5. Microbial Species

The dominant bacterial biomarker in the soil treated with PAL was Koribacteraceae (as shown in Table 3 and Figure S1). The main bacterial biomarker in the soil treated with BAS was Caulobacteraceae. The dominant bacterial biomakers in the soil treated with CCH were mainly Solirubrobacterales, Rhizobiales, Rhodospirillales, and Alphaproteobacteria. The Acidobacteriota shows a negative correlation with Chloroflexi and Actinobacteriota. In contrast, Acidobacteriota has a positive correlation with Myxococcota. Additionally, Chloroflexi is positively correlated with Proteobacteria (including Aquicella, Reyranella, and Pseudomonas) (Figure S2). There were abundant fungi biomarkers in the soil treated with PAL, which were mainly Chrysozymaceae, Trimorphomycetaceae, and Tremellales. The fungi biomakers of soil treated with BAS were Aspergillaceae, Onygenales, and Ceratostomataceae. In addition, the fungi biomakers of soil treated with CCH were Botryosphaeriales, Didymellaceae, Xylariales, and Sebacinaceae (as shown in Table 3 and Figure S3). At the level of Genus, Puccinia has a negative correlation with Umbilicaria. Ganoderma also has a negative correlation with Humicola (Figure S4). The main biomarkers in the soil treated with OF were more than those of other treatments (Figures S1 and S3).
The Venn diagram analysis (Figure 7) revealed substantial differences in the number of bacterial specific operational taxonomic units (OTUs) across various soil treatments. The soil treated with OF exhibited 799 bacterial-specific OTUs, a significantly higher count compared to soils treated with CCH, PAL, and BAS. Notably, the soils treated with PAL and BAS had 57 and 89 bacterial-specific OTUs, respectively. The relatively close value between the PAL-treated and BAS-treated soils suggests similarities in their bacterial communities in this regard. It may be because the material composition and decomposition characteristics of PAL and BAS are similar. The highest OTUs of endemic fungi were found in the mixed soil treated with CCH, followed by the soil cultured without organic materials, and the OTUs of endemic fungi were closer in the soil treated with PAL and BAS. In addition, soil endemic bacteria OTUs and endemic fungi OTUs without exogenous organic material input were higher than those of PAL and BAS.
Shannon of bacteria and fungi was shown in Figure 8. The Shannon index of both bacteria and fungi in the soil of CK was relatively higher than PAL and BAS. The Shannon index of both bacteria and fungi in the soil treated with PAL and BAS was significantly lower than those in CCH and OF. However, there was no significant difference in the Shannon index of bacteria and fungi between the soils treated with PAL and BAS. This phenomenon indicated that soil could maintain its own microbial community structure stability within a certain range under the condition of no exogenous interference. The input of exogenous organic materials stimulates the activity of microorganisms and increases their absorption and transformation of nutrients. Under the condition that there is no continuous input of exogenous materials, with the extension of culture time, microorganisms will compete for nutrients, resulting in insufficient nutrient supply, and some competitive and adaptable bacteria will be eliminated.

4. Discussion

4.1. Effects of Organic Material Composition on Soil pH and Organic Acid Content

Soil properties such as pH, electrical conductivity (EC), and organic acid content are crucial for maintaining soil fertility and the growth environment of plants. The composition of organic materials can significantly impact these soil properties through various physical, chemical, and biological processes. Some organic materials can lower soil pH. In this study, the decomposition of PAL to produce organic acids (isobutyric, isovaleric, and hexanoic acids) in the short term significantly reduced soil pH value compared with CK and OF (Table 2). This phenomenon is mainly because plant residues are rich in tannins and organic acids. The tannins are gradually broken down by soil microorganisms, and the chemical reactions involved result in the production of acidic substances [26]. Additionally, the organic acids directly contribute to the increase in hydrogen-ion concentration in the soil, thus reducing the soil pH. In contrast, organic materials with a high content of basic cations can increase soil pH. Animal manures, such as cow manure, often contain significant amounts of Ca, Mg, and K [27]. BAS and OF contain a lot of Ca and Mg [28], which can supplement the exchangeable Ca and Mg in the soil and improve the soil pH value (Table 2).
The addition of organic materials can affect soil EC [28]. Organic materials that are rich in soluble salts or release a large number of ions during decomposition can increase soil EC [29]. In this study, the input of PAL significantly increased the contents of isobutyric acid, isovaleric acid, and caproic acid in the soil at the early stage of culture, thus intensifying the acidification of the soil at the early stage compared with CK (Table 2 and Figure 1). This is mainly because the composition of organic materials determines the types and amounts of organic acids produced during decomposition. In addition, organic matter (for example, PAL) is rich in simple carbohydrates and proteins and can produce various organic acids [30].

4.2. Effect of Organic Materials on Aggregate Formation and the Distribution of Carbon and Nitrogen Content in Aggregates

The formation of >0.25 mm aggregates in this study may also be influenced by the content of Ca and Mg in PAL, BAS, and CCH (Table 2). The formation of soil aggregates is a complex and dynamic process, influenced by a multitude of factors, among which the composition of organic materials stands out as a key determinant [31,32]. Plant residues, such as crop straws, green manure, and forest litter, are rich in a variety of organic components [32,33]. A study in a wheat–maize rotation system indicated that straw returning (maize straw returning and wheat straw returning) resulted in a significantly higher mean weight diameter than that for no straw returning [34]. In this study, the input of organic materials also a significantly increased the formation of soil aggregates >0.25 mm (Figure 2), and the relevant research results were similar to those of other studies [35,36]. Cations can form metal-humus complexes, which act as strong bridges between soil particles. These complexes can withstand mechanical forces and water erosion, thus enhancing the stability of soil aggregates. Soil aggregates are crucial for maintaining soil structure and fertility, and the C and N allocation within them significantly affects soil-related ecological processes. Organic materials, with their diverse compositions, play a fundamental role in regulating the C and N distribution in soil aggregates [37]. Plant residues, such as crop straws, green manure, and biochar, can introduce substantial amounts of C and N into the soil [37,38,39]. In this study, the input of typical tropical organic materials also significantly increased the content of carbon and nitrogen in aggregates of different particle sizes (Figure 3). This is mainly because when organic materials decompose, they release a large amount of soluble organic carbon and nitrogen, which are quickly taken up by soil microorganisms within the aggregates [40,41].

4.3. Effect of Organic Material Input on Organic Carbon Structure of Soil Aggregates

Organic material input represents a crucial strategy for enhancing soil organic carbon content and improving soil structure. Soil aggregates exhibit diverse particle-size distributions, with each fraction demonstrating distinct capacities for fixing and transforming organic carbon [42,43]. In this study, the vibration of the functional groups in the aggregates < 0.053 mm was significantly weakened under the treatment of other organic materials, except that of OF and CK. Compared with CK, organic materials (PAL, BAS, CCH, and OF) enhanced the vibration of C=C/N=H and –OH/C–H functional groups in 0.053–0.25 mm soil aggregates, which significantly influence soil C cycling and fertility [44].
Following the addition of organic materials, the relative contents of alkyl carbon (–C–C–) and alkoxy carbon (–C–O–) functional groups in large aggregates typically increase [36]. These functional groups contribute to the stability of organic carbon due to their resistance to microbial decomposition [45]. Conversely, the content of aromatic carbon (–C=C–) may experience a relative decline. This phenomenon is mainly because the influx of fresh carbon sources from organic materials dilutes the relatively stable aromatic-structured carbon initially present in large aggregates [46].

4.4. Effects of Differences in Organic Material Composition on Microbial Groups

Soil microorganisms are the engine driving various biogeochemical processes in the soil, and their community composition and function are closely related to the quality and quantity of organic materials in the soil. In this study, the input of CCH and OF significantly increased the types of soil microorganisms, which may be mainly affected by the composition of these materials. The composition of organic materials can vary greatly, and these differences have significant impacts on the structure and function of microbial communities [47]. The C:N ratio of organic materials is a key factor influencing microbial communities. Organic materials with a low C:N ratio, such as fresh legume residues, may favor the growth of bacteria [47,48]. Organic materials rich in simple sugars and starches, such as molasses and some types of root crop residues, can quickly stimulate the growth of bacteria [49].
Organic materials containing complex polymers, such as lignin-rich forest litter and some types of crop straw, are more suitable for the growth of specific microbial groups. In this study, the input of CCH significantly increased the OTUs of fungi at the later stage of culture (Figure 7), mainly because CCH is rich in lignin, and the decomposition of lignin is closely related to fungi [50]. In conclusion, the composition of organic materials has a profound impact on microbial groups in the soil. Understanding these relationships can help us better manage soil ecosystems, for example, by choosing appropriate organic materials to promote the growth of beneficial microorganisms and improve soil fertility. However, more research is still needed to fully understand the complex interactions between organic material composition and microbial communities, especially under different environmental conditions.

5. Conclusions

Soil acidification in the short term with the application of PAL is mainly due to the significant increase in isobutyric acid, isovaleric acid, and hexanoic acid. PAL and BAS can promote the formation of soil aggregates in a short period of time. CCH and OF have a better effect on the formation of soil aggregates in the long term. The input of organic materials mainly changes the organic carbon structure in large aggregates in the short term. The soil microbial community structure in the treatments of CCH and OF is relatively rich. In the absence of external interference, the soil can maintain the stability of its own microbial community structure within a certain range. Therefore, according to actual needs, various organic substances can be mixed and returned to the field, enabling them to play their unique roles in soil improvement, respectively. In the future, it is necessary to carry out long term field experiments on the return of typical tropical organic materials to the field to observe the long term changing patterns of the impacts of returning organic materials to the field on the physical and chemical properties and microorganisms of laterite in tropical regions.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy15051073/s1, Figure S1. The cladogram of bacteria, Figure S2. The p_network of bacteria, Figure S3. The cladogram of fungi, Figure S4. The p_network of fungi.

Author Contributions

Conceptualization, S.S.; Data curation, S.L. and Y.L.; Funding acquisition, S.S. and H.M.; Methodology, S.S., S.L. and Y.L.; Software, S.L. and Y.L.; Supervision, S.S.; Visualization, S.S.; Writing—original draft, S.S.; Writing—review and editing, S.S., W.S. and H.M. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by Key R&D Program Projects in Guangdong Province (2023B0202010027), Guangdong Basic and Applied Basic Research Foundation (2025A1515010862), Central Public-interest Scientific Institution Basal Research Fund (1630062022004), and Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center (CATASCXTD202303).

Data Availability Statement

The original contributions presented in this study are included in the article/Supplementary Materials. Further inquiries can be directed to the corresponding author(s).

Conflicts of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Figure 1. Changes in soil organic acid content.
Figure 1. Changes in soil organic acid content.
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Figure 2. Changes of aggregate structure ((A): 90 d; (B): 270 d; (C): 540 d; (D): 1080 d) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
Figure 2. Changes of aggregate structure ((A): 90 d; (B): 270 d; (C): 540 d; (D): 1080 d) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
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Figure 3. Distribution of C and N in soil aggregates ((A,C): the C and N content in different soil aggregates at 90 days; (B,D): the C, N content in different soil aggregates at 1080 days) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
Figure 3. Distribution of C and N in soil aggregates ((A,C): the C and N content in different soil aggregates at 90 days; (B,D): the C, N content in different soil aggregates at 1080 days) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
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Figure 4. Change of δ13C/δ15N in each aggregate (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
Figure 4. Change of δ13C/δ15N in each aggregate (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
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Figure 5. Fourier transform infrared spectra of soil aggregates at 90 days ((a): <0.053 mm; (b): 0.053–0.25 mm; (c): 0.25–2 mm; (d): >2 mm).
Figure 5. Fourier transform infrared spectra of soil aggregates at 90 days ((a): <0.053 mm; (b): 0.053–0.25 mm; (c): 0.25–2 mm; (d): >2 mm).
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Figure 6. Fourier transform infrared spectra of soil aggregates at 1080 days ((a): <0.053 mm; (b): 0.053–0.25 mm; (c): 0.25–2 mm; (d): >2 mm).
Figure 6. Fourier transform infrared spectra of soil aggregates at 1080 days ((a): <0.053 mm; (b): 0.053–0.25 mm; (c): 0.25–2 mm; (d): >2 mm).
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Figure 7. The Venn diagram of bacteria and fungi.
Figure 7. The Venn diagram of bacteria and fungi.
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Figure 8. The Shannon of bacteria (A) and fungi (B) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
Figure 8. The Shannon of bacteria (A) and fungi (B) (Note: Different lowercase letters indicate significant differences (p < 0.05) among treatments).
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Table 1. C, N content of organic materials and the amount of organic materials and (NH4)2SO4.
Table 1. C, N content of organic materials and the amount of organic materials and (NH4)2SO4.
Organic MaterialC Content/%N Content/%C/Nδ13Cδ15NAmount of Organic Materials/gAmount of (NH4)2SO4/g
PAL41.790.5773.31−14.630.2211.960.62
BAS37.780.34111.12−24.055.0513.230.73
CCH27.930.19147.00−27.424.1817.900.78
OF27.472.3511.69−21.096.1218.200.00
Table 2. Changes of soil pH/EC and exchangeable Ca and Mg in soil.
Table 2. Changes of soil pH/EC and exchangeable Ca and Mg in soil.
TreatmentpHECCa Mg
μs/cmmg/kg
90 dPAL4.76 ± 0.02 d174.87 ± 42.7 a35.00 ± 5.77 b6.10 ± 0.01 b
BAS5.13 ± 0.12 b166.17 ± 26.97 a47.50 ± 5.00 a15.25 ± 4.31 a
CCH4.44 ± 0.08 e189.64 ± 31.57 a32.50 ± 5.00 bc15.25 ± 4.31 a
OF6.93 ± 0.04 a116.84 ± 7.17 b27.50 ± 5.00 c10.68 ± 3.05 ab
CK4.94 ± 0.06 c63.31 ± 7.21 c20.00 ± 0.01 d6.10 ± 0.01 b
1080 dPAL4.80 ± 0.04 bc46.82 ± 2.70 b25.00 ± 4.08 a9.18 ± 2.49 a
BAS4.76 ± 0.11 c76.32 ± 3.59 a23.33 ± 4.71 a8.13 ± 2.88 ab
CCH5.23 ± 0.16 a42.00 ± 2.25 b10.00 ± 0.01 c6.10 ± 0.01 b
OF5.28 ± 0.02 a58.03 ± 23.16 ab15.00 ± 4.08 bc6.10 ± 0.01 b
CK4.92 ± 0.09 b50.38 ± 19.82 b16.68 ± 4.71 b6.10 ± 0.01 b
Note: Data are means ± standard error, n = 4. Different lowercase letters indicate significant differences (p < 0.05) among treatments.
Table 3. The main biomarkers of bacteria and fungi.
Table 3. The main biomarkers of bacteria and fungi.
TreatmentBacterial BiomarkersFungi Biomakers
PALKoribacteraceaeChrysozymaceae, Trimorphomycetaceae, and Tremellales
BASCaulobacteraceaeAspergillaceae, Onygenales, and Ceratostomataceae
CCHSolirubrobacterales, Rhizobiales, Rhodospirillales, and AlphaproteobacteriaBotryosphaeriales, Didymellaceae, Xylariales, and Sebacinaceae
OFBlastocatellaceae, Gaiellaceae, Bacillaceae, Paenibacillaceae, et al.Dothideomycetes, Diaporthaceae, Stephanosporaceae, et al.
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Song, S.; Liu, S.; Liu, Y.; Shi, W.; Ma, H. Effects of Tropical Typical Organic Materials on Soil Physicochemical Properties and Microbial Community Structure. Agronomy 2025, 15, 1073. https://doi.org/10.3390/agronomy15051073

AMA Style

Song S, Liu S, Liu Y, Shi W, Ma H. Effects of Tropical Typical Organic Materials on Soil Physicochemical Properties and Microbial Community Structure. Agronomy. 2025; 15(5):1073. https://doi.org/10.3390/agronomy15051073

Chicago/Turabian Style

Song, Shuhui, Siru Liu, Yanan Liu, Weiqi Shi, and Haiyang Ma. 2025. "Effects of Tropical Typical Organic Materials on Soil Physicochemical Properties and Microbial Community Structure" Agronomy 15, no. 5: 1073. https://doi.org/10.3390/agronomy15051073

APA Style

Song, S., Liu, S., Liu, Y., Shi, W., & Ma, H. (2025). Effects of Tropical Typical Organic Materials on Soil Physicochemical Properties and Microbial Community Structure. Agronomy, 15(5), 1073. https://doi.org/10.3390/agronomy15051073

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